The molecular basis of morphological evolution has been a long standing topic of interest in evolutionary biology, but a mechanistic understanding of this process has been elusive. The male genital posterior lobe exhibits substantial variation in size between the recently diverged (0.6 - 0.9 million years) species of Drosophila simulans and D.mauritiana, and there is a large amount of background work describing the genetic architecture of this trait. Several QTL have already been localized to narrow chromosomal intervals, have largely additive effects, and the direction of these effects are consistent across loci, which suggests a history of strong directional selection. The goals of the proposed research are to: 1) identify at least one gene that explains a significant portion of the interspecific variation 2) identify the cis-regulatory sequence for that gene, 3) characterize the pattern of gene expression in each species, and 4) determine the molecular basis of functional sequence divergence at that locus. I will begin idenfication of the target gene by crossing males of both D. simulans and D. mauritiana to deficiency stocks and alleles of genes from D. -melanogaster, for a subset of QTL intervals, to identify loci that fail to complement phentypic recovery of a hybrid phenotype. If this method fails to identify any target loci, I will create congenic lines to use linkage disequilibrium mapping and potentially p-element mediated site specific recombination to localize a single target gene. Once a gene has been identified I will idenfity the cis-regulatory element that drives it's expression in the genital disc and examine variation in gene expression between the three species to determine if cis-regulatory evolution is responsible for the observed differentiation. Finally, I will use population genetic methods to identify specific regions in the protein coding and regulatory sequences that have evolved under positive selection. [unreadable] [unreadable]